The solution to this problem is to have a shared core of libraries which change slowly enough that they can be reasonably dumped into the install media of the linux distribution itself, and frozen afterwards (in terms of functionality/abi). This cuts down the number of libraries you do have to bring with the application bundles, and defines a common binary interface for all software. In practice this requires very strict and careful maintenance, and ideally we could get a common set of baseline binaries ("linux core version 1") shipped by all distributions.
Secondly, the application bundles should provide multiple applications. For instance, if you were to install new version of KDE or GNOME by the application bundle method, it better all be in 1 bundle. This, in turn, makes it possible to ship shared libraries in the bundle, and therefore reaping the memory saving benefits, and therefore it is probably the method that the Calligra suite should be using. Maybe some amount of system dependencies would be acceptable, such as X libraries or glibc, to limit the size of the bundle somewhat. (Just handwaving the problems away here, obviously. It's difficult to do until we get the "linux core version 1" defined and deployed.)